How can you specify that you want a rectangle area to be above the ground? Whenever I create them, they are always at ground level. I want to build ones that you could fly under.

Just raise them up. :)You can specify an altitude in one of the text fields defining the properties for the area or you can use the center mouse button (may need to press the mouse wheel).It's covered in the SDK and in the mission building articles on FSinsider.